Resumen (Viruses from Hell (and beyond)):
Viruses are the most abundant and diverse biological entities on Earth. Viruses outnumber all organisms by at least an order of magnitude, are far more genetically diverse than cellular organisms and are found in all environments examined to date. Viruses found in high temperature (>70C) acidic (pH <3) environments have unique genomes and morphology. The most common of these viruses are the fusiform or spindle-shaped viruses, which have been found in volcanic hot springs world-wide. The best-studied of the fusiform viruses are the SSVs, Sulfolobus spindle-shaped viruses. We have also found isosahedral viruses whose structures indicate conservation of structure since the divergence of archaea bacteria and eukarya, probably 3 billion years ago.
We have recently shown that some viruses can be coated in silica as a potential first step towards conservation in the geologic record. These viruses lose activity very rapidly upon silicification but, under appropriate conditions, can be reactivated. Moreover silicified viruses are very resistant to dessication, providing a potential explanation for virus dispersal and a possible new route to vaccine formulation.
A recent viral metagenome survey of an acidic hot lake (>50C, pH 2) in Lassen Volcanic National Park, USA, revealed not only sequences similar to the SSVs and other known thermoacidophilic viruses, but also a unique viral genome that appears to have arisen by unprecedented DNA-RNA recombination (Diemer and Stedman, 2012). Portions of this novel virus genome type have been detected in many environments. Recently 4 other similar complete genomes have been elucidated. The widespread nature of these “hybrid” viruses and a number of novel possible mechanisms for their origin will be discussed.
(Diemer GS, and Stedman KM. (2012) A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses. Biol Direct. 2012 Jun 11;7:13. doi: 10.1186/1745-6150-7-13.)

Resumen (PhageFISH - visualizing intracellular and free viruses):
Microbes drive the biogeochemical cycles that fuel planet Earth, and their viruses (phages) alter microbial population structure, genome repertoire, genetic make-up and metabolic capacity. However, our ability to understand and quantify phage-host interactions is technique-limited. Here, we introduce phageFISH – a markedly improved geneFISH protocol that increases gene detection efficiency from 40% to >92% and is optimized for detection and visualization of intra- and extracellular phage DNA. The application of phageFISH to characterize infection dynamics in a marine podovirus-gammaproteobacterial host model system corroborated classical metrics (qPCR, plaque assay, FVIC, DAPI) and outperformed most of them to reveal new biology. PhageFISH detected both replicating and encapsidated (intracellular and extracellular) phage DNA, while simultaneously identifying and quantifying host cells during all stages of infection. Additionally, phageFISH allowed per-cell relative measurements of phage DNA, enabling single-cell documentation of infection status (e.g., early vs late stage infections). Further, it discriminated between two waves of infection, which no other measurement could due to population-averaged signals. Together, these findings richly characterize the infection dynamics of a novel model phage-host system. Moreover, these findings debut phageFISH as a much needed tool for studying phage-host interactions in the laboratory, with great promise for environmental surveys and lineage-specific population ecology of free phages, including those found in acidic environments.